`matrixORMatrix-class.Rd`

The Milo container class

`graph`

An igraph object that represents the kNN graph

`nhoods`

A list of neighbourhoods as graph indices and their constituent single cells

`nhoodDistances`

An list of PxN sparse matrices of Euclidean distances between vertices in each neighbourhood, one matrix per neighbourhood

`nhoodCounts`

An NxM sparse matrix of cells counts in each neighourhood across M samples

`nhoodIndex`

A list of the index vertices for each neighbourhood

`nhoodExpression`

An GxN matrix of genes X neighbourhoods containing average gene expression levels across cells in each neighbourhood

`nhoodReducedDim`

a list of reduced dimensional representations of neighbourhoods, including projections into lower dimension space

`nhoodGraph`

an igraph object that represents the graph of neighbourhoods